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Yorodumi- PDB-4jcc: Crystal structure of iron uptake ABC transporter substrate-bindin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jcc | ||||||
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Title | Crystal structure of iron uptake ABC transporter substrate-binding protein PiuA from Streptococcus pneumoniae Canada MDR_19A | ||||||
Components | Iron-compound ABC transporter, iron-compound-binding protein | ||||||
Keywords | TRANSPORT PROTEIN / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES / ALPHA AND BETA PROTEIN / PERIPLASMIC BINDING PROTEIN TYPE III FOLD / IRON TRANSPORT / IRON UPTAKE ABC TRANSPORT SYSTEM SUBSTRATE BINDING PROTEIN / PUTATIVE MEMBRANE-ANCHORED LIPOPROTEIN | ||||||
Function / homology | Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / ISOPROPYL ALCOHOL / : Function and homology information | ||||||
Biological species | Streptococcus pneumoniae (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.133 Å | ||||||
Authors | Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of iron uptake ABC transporter substrate-binding protein PiuA from Streptococcus pneumoniae Canada MDR_19A Authors: Stogios, P.J. / Wawrzak, Z. / Kudritska, M. / Yim, V. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jcc.cif.gz | 172.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jcc.ent.gz | 136.6 KB | Display | PDB format |
PDBx/mmJSON format | 4jcc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4jcc_validation.pdf.gz | 453 KB | Display | wwPDB validaton report |
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Full document | 4jcc_full_validation.pdf.gz | 455.5 KB | Display | |
Data in XML | 4jcc_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 4jcc_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/4jcc ftp://data.pdbj.org/pub/pdb/validation_reports/jc/4jcc | HTTPS FTP |
-Related structure data
Related structure data | 2chuS S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 31071.398 Da / Num. of mol.: 1 / Fragment: UNP residues 37-321 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: Canada MDR_19A / Gene: MYY_1766 / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: H8LJX2 | ||||
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#2: Chemical | ChemComp-CL / | ||||
#3: Chemical | #4: Chemical | ChemComp-IPA / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.43 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6 Details: 2.5 M ammonium sulphate, 0.1 M sodium acetate pH 4.6, 2% isopropanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 9, 2012 |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97856 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→31.52 Å / Num. obs: 95947 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 5.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.13→1.18 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.561 / Mean I/σ(I) obs: 2.7 / Num. unique all: 11431 / % possible all: 96.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2CHU Resolution: 1.133→31.52 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.39 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.133→31.52 Å
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Refine LS restraints |
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LS refinement shell |
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